neat stuff - I've also learned about the existence and usage of libHaru pdf library
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Very Lightweight And Fast Genomic Bed Viewer
I deal a lot with bed files on hg19. Is there a very lightweight, no fuss, very fast viewer to do:
./viewer [bed file in] [pdf file out]
and you could view distribution of the ranges in the pdf file similar to something like this: http://cistrome.dfci.harvard.edu/CaSNP/gscore/ I do not want to open a graphical user interface for a genome browser each time I apply a tiny little filter.
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Dear myself, It's me, you.
I made this for you: https://github.com/grenaud/bedBamAndBeyond
That creates images as such: https://github.com/grenaud/bedBamAndBeyond/blob/master/example.png
It has some horrible inefficiencies in the code that I will clean at some point. It should allow for BAM files as well.
Have fun with it.
You
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What do you mean by "distribution of ranges"? A histogram of feature sizes? Or each line in the BED file placed on a chromosome? Can you give an example of what you want to have in the PDF?
something simple along those lines :http://cistrome.dfci.harvard.edu/CaSNP/gscore/
Have you tried the answers at Drawing chromosome ideogams with data? In particular, the second plot in this answer: A: Drawing chromosome ideogams with data
They are all R packages, hasn't someone build either a wrapper or something faster and easier to use ?